HIV-1 protease is the target of the most effective anti-viral drugs for the treatment of HIV-1 infection. All these drugs derive from successful structure-based design studies. The enzyme cleaves the viral gag-pol polyprotein ten unique sites and is essential for maturation of the virion and thus the spread of the virus. Therefore, it has been a prime target for drug design research. Unfortunately the medical efficacy of the current drugs are proven to be short lived, as viable mutant variants of HIV-1 protease confer drug resistance. Drug resistance is a subtle change in the balance of recognition events, between the relative affinity of the enzyme to bind inhibitors and it ability to bind and cleave substrates. Since HIV-1 protease binds substrates and inhibitors at the same active site a change that alters inhibitor binding also alters substrate binding. We hypothesize that this change will select I alternate substrate sequences. The goal of this study, in addressing this hypothesis, is to elucidate and analyze sequence, kinetic and/or structural changes occurring in the substrates, proteases and inhibitors that coincide w drug resistance. To accomplish this goal we are: (i) obtaining sequence data from patients whose protease gene shows drug resistance and from phage display screening techniques; (ii) performing basic kinetic assays and (i solving high resolution crystal structures of substrate complexes. These data, when taken together, will help guide the effort of the scientific and pharmaceutical community to design and develop second generation drugs